Methods and systems to assess clogging from bacteria associated with a first well are disclosed. The first well is maintained in a quiescent state for a first period of time. Water is not pumped from the first well in the quiescent state. A pump attached to the first well is turned to an ON state. Water is pumped from the first well during the ON state. A water sample is received from the first well during the ON state. The water sample is collected during a first time period corresponding to a surge in mobile particles. A first activity level for a first type of bacteria in the water sample is determined. The activity level is analyzed for clogging specific information related to a state of clogging associated with the first well.